Ivan Rogers has a point. Indeed, he is right three times over. First, it is not the job of civil servants passively to execute ideas put up by Ministers that simply won’t work. They should, as he puts it in his resignation letter, “challenge ill-founded arguments and muddled thinking” and “never be afraid to speak the truth to those in power”. These are not breaches of institutional ethos. They are baseline requirements of it.

Second, it would have made no sense to have an EU Ambassador in place who quit just as negotiations began in earnest. Rogers’s resignation has prevented this from happening. As matters stood before he quit, he was due to leave his post in October – almost exactly the time when the talks, in the wake of Germany’s elections, are likely to gather pace. As he says in his letter, it is best if a new ambassador is in place when Article 50 is moved, and stays in post until the formal negotiation is finished.

Finally, a lot of the briefing against him has been unfair. Much of has clearly come from former SpAds in David Cameron’s Downing Street. The nub of it is that, had Rogers’s advice been rejected, a successful renegotiation would have been achieved. This suggests that had Cameron asked for, say, an emergency brake on EU immigration, he would have got it. At best, this is wishful thinking. At worst, it is buck-passing. There is nothing in Angela Merkel’s history to date which suggests that she, and other EU leaders with her, would have been willing to put the sacred cow of free movement to the slaughter.

Indeed, Rogers seems to be as sceptical about the European project as any senior civil servant working in the field is capable of being. “Ivan’s scorn for the right of the Tory Party seemed only rivaled by his hatred of the European leaders and officials who, in his view, hadn’t understood that they were heading for a fall,” writes Daniel Korski, one of the clearest-eyed of those SpAds. “He could be infuriating, but he was right on many of the big issues, including that what the Conservative Party was asking for was not something that European leaders would ever agree to provide.”

But although Roger’s head is the right place, his heart doesn’t seem to be. The long and the short of it is that he appears to be out of sympathy with Brexit – as illustrated by his claim that it will take ten years to finalise a trade deal. You may reply that the ways in which the hearts of civil servants are inclined is not the business of Ministers. This is a misunderstanding of the way in which the civil service should work – and has, and does.

Yes, civil servants should challenge Ministers if their plans are impracticable. But this is a matter of delivery, not aim. It is an illusion to believe that the civil service is, or has ever been, a fount of the purest neutrality. It must have institutional biases if it is to do its job. Take policy. During the early 1990s, the Treasury threw its institutional weight behind the ERM. This wasn’t because of pro-EU bias. (The department turned out to be as opposed to Britain joining the Euro as it was supportive of it joining the ERM.) Rather, it was because the Treasury needed a star to steer by in order to avoid the perils of inflation.

You may or may not believe that the means was mistaken. But whether so or not, the department staked its standing on a policy, and saw it shrivelled when Britain was forced out of the mechanism. Or consider people. Michael Quinlan was one of Whitehall’s foremost post-war policy experts. A senior civil servant at the Ministry of Defence, he was “a strong believer in the value of deterrence”, as the Guardian‘s obituary put it. No impartiality there. Sir Michael would have been lost had a Labour Government prepared to downgrade that defence taken power – let alone abandoned our nuclear weapons unilaterally.

Now return to the biggest policy issue of all. In his This Blessed Plot, the late Hugo Young, who perhaps qualifies as the most committed journalist in recent history to the EU project, lovingly details how the Foreign Office made the journey from aloof Eurosceptism to passionate Euroenthusiasm – from Roger Makins through John Robinson through Michael Palliser to the Stephen Walls and John Kerrs and David Hannays of the present day. No neutrality here, either. No turning of the Foreign Office’s back on taking an institutional view.

This is the crux of the matter – not only for King Charles Street, but for the whole of Whitehall. The British people have voted to leave the EU, on a large turnout and in large numbers: the vote for Brexit was bigger than the vote delivered to any political party since the war. It marks a cultural sea-change in British politics so big that the country has not yet collectively come to terms with it.

The changing of the weather has sunk some big ships. David Cameron has slipped below the water. Michael Gove has come close to scuttling his own ship. George Osborne is not drowning, but waving – or it the reverse? But the big damage is less personal than institutional. The referendum result was a torpedo for the Foreign Office. It has lost responsibility for the EU negotiation altogether. It is in a state of mourning so acute that Boris Johnson has been sent in to cheer it up, not to mention get it ship-shape again. Much of Rogers’s note is actually a defence of the interests of UKREP against those of others, especially in the Exiting the European Union department.

“Ivan Rogers huge loss. Can’t understand wilful & total destruction of EU expertise, with Cunliffe, Ellam & Scholar also out of loop. #amateurism”, tweeted Nick Macpherson, until recently Permanent Secretary at the Treasury. This showed how deep sympathy for Rogers runs in parts of Whitehall. Watching the back of one’s colleagues is one thing. But thumbing one’s nose at the biggest electoral mandate in recent history would be quite another. The civil service adapted to the end of the ERM; now it must adapt to leaving the EU. Senior civil servants are tough and clever enough to take the heat in the kitchen. But if they simply can’t stand what the chef is serving up – at the express request of the customers – it’s everyone’s interest, not least their own, for them to get out of it.